Contents


CHARTS AND TABLES

Input Elements Output Elements
PlateView Manipulate samples
Heatmap Overview of all samples and probes
Experiment Table
Manipulate experiments
Bargraph
Show probes and/or samples
Sample Table
Manipulate samples
Differential Expression Table
Show p-value ranked differential expression
Probe Table
Manipulate probes
Variable Data Chart
Show selected probes broken out by group
Variable Table
Manipulate variables
Volcano Plot
Show p-value / fold expression chart
Pair Plot
Compare a pair of probes or samples
Stability Plot
Probe suitability for normalization

GUI ELEMENTS

The different elements are labeled on a screenshot.
Buttons Other actions
Load Button
Bring data from disk into memory
Menus
The top menu bar
Experiment Button
Create experiments
FDE
Quick access to the Firefly Discovery Engine
Negative Button
Mark negative samples
Selection Selecting probes, samples, experiments
Normalize Button
Toggle normalization status
Zoom & pan Moving around charts
Export Button
Save data from memory back to disk
Tables
General info about tables
Clear Button
Empty memory
Variable Definition
How to define variables
Features and modes
Switching assay or feature level




DATA CONCEPTS

Files Concepts
FCS file Flow cytometry data Work flow Samples vs plates vs experiments
FWS file Firefly workspace Experiment Group of samples for statistical processing
PLX file
Barcoded probe definition
Plate Group of samples for visual selection
Sample Sheet
Plate layout definition
Variable Basis for differential analysis

Standard Curve

Quantification using known standards
LoD Limit of detection


Sample quality Data quality in a particular sample



ALGORITHMS

Data Processing
Calculating target levels in each sample from flow cytometry events
Data Statistics
How the mean, standard deviation and confidence intervals are calculated
Normalization
Motivation, algorithms and experience with normalization
Clustering
Hierarchical clustering used to organize the heatmap
Differential Analysis
Using variables to analyze differential expression between groups of samples
Multiple Comparisons
Calculating p-values in a multiplex context
Anova with repeated measures
Differential analysis of a primary variable, controlling for secondary variables.
Standard Curves
Absolute quantitation using known standards
Extended Range
Rescuing a dataset with saturated signal